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Hi Jarrod
here are the scripts:
phylo<-read.nexus("output.nex")
phylo$edge.length <- phylo$edge.length[1 + .0000001]
phylo_ultra=chronos(phylo, lambda=0)
is.ultrametric(phylo_ultra)
tree.unmatched <- multi2di(phylo_ultra, random=TRUE)
plotTree(tree.unmatched,fsize=0.6)
inv.phylo<-inverseA(tree.unmatched,nodes="TIPS",scale=TRUE)
When I do plotTree, I can visualise the tree.
but the original file looks like a list, here is just an extract of the
original file output.nex:
#NEXUS BEGIN TREES; TREE tree_2467 =
((Anguilla_anguilla:274.35321211,(((Oreochromis_tanganicae:128.00000000,((Channa_argus:94.28562300,((Scophthalmus_maximus:64.40000000,Paralichthys_dentatus:64.40000000)'14':19.14618300,Seriola_quinqueradiata:83.54618300)'13':10.73944000)'11':15.71437700,(((Gasterosteus_aculeatus:94.90000000,Perca_flavescens:94.90000000)'10':15.10000000,((Siganus_vulpinus:99.80000000,(Lutjanus_peru:99.80000000,Argyrosomus_regius:99.80000000)'19':0.00000000)'9':10.20000000,Sparus_aurata:110.00000000)'22':0.00000000)'8':0.00000000,(Zosterisessor_ophiocephalus:56.20000000,Ponticola_eurycephalus:56.20000000)'6':53.80000000)'30':0.00000000)'29':18.00000000)'27':78.33545792,((Salmo_salar:12.51368429,Salmo_trutta:12.51368429)'35':33.20842500,Oncorhynchus_mykiss:45.72210929)'43':160.61334863).........;END;
thanks!
d
PS. If I drop TIPS, I have the same message.
____________________________________________________________
David Costantini
Professor of Conservation Physiology
Muséum National d'Histoire Naturelle, CNRS
7 rue Cuvier
75005 Paris, France
Tel.: +33.(0)1.40.79.53.74
Associate Editor Functional Ecology
http://davidcostantini.wordpress.com/
https://twitter.com/DavidZool
http://scholar.google.com/citations?user=nBSC4-EAAAAJ&hl=it
----- Original Message -----
From: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk>
To: "David COSTANTINI" <david.costant...@mnhn.fr>, "r-sig-phylo"
<r-sig-phylo@r-project.org>
Sent: Monday, 17 May, 2021 19:48:59
Subject: Re: [R-sig-phylo] phylogenetic correction and MCMC model
Hi David,
It looks like phylo_ultra might be a list? Is phylo_ultra[[1]] a tree?
Also, don't use nodes="TIPS"; this is just to demonstrate how poor the
algorithm is when you don't use the expanded inverse. I see people using
nodes="TIPS" a lot - where does this code come from?
Cheers,
Jarrod
On 17/05/2021 16:06, David Costantini wrote:
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Dear All
I am trying to apply a phylogenetic correction to an MCMC model, but I have
problems in making the inverse matrix. I can visualise the treeplot very well,
but when I use the script:
inv.phylo<-inverseA(phylo_ultra,nodes="TIPS",scale=TRUE)
R tells me that there is an error:
Error in pedigree[, 2] : incorrect number of dimensions
In addition: Warning message:
In if (attr(pedigree, "class") == "phylo") { :
Do you have any experience with this? I couldn't find a solution so far.
Thanks in advance
David
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